mirror of https://github.com/msberends/AMR.git
93 lines
2.9 KiB
R
93 lines
2.9 KiB
R
% Generated by roxygen2: do not edit by hand
|
|
% Please edit documentation in R/ab_class_selectors.R
|
|
\name{antibiotic_class_selectors}
|
|
\alias{antibiotic_class_selectors}
|
|
\alias{ab_class}
|
|
\alias{aminoglycosides}
|
|
\alias{carbapenems}
|
|
\alias{cephalosporins}
|
|
\alias{cephalosporins_1st}
|
|
\alias{cephalosporins_2nd}
|
|
\alias{cephalosporins_3rd}
|
|
\alias{cephalosporins_4th}
|
|
\alias{cephalosporins_5th}
|
|
\alias{fluoroquinolones}
|
|
\alias{glycopeptides}
|
|
\alias{macrolides}
|
|
\alias{penicillins}
|
|
\alias{tetracyclines}
|
|
\title{Antibiotic class selectors}
|
|
\usage{
|
|
ab_class(ab_class)
|
|
|
|
aminoglycosides()
|
|
|
|
carbapenems()
|
|
|
|
cephalosporins()
|
|
|
|
cephalosporins_1st()
|
|
|
|
cephalosporins_2nd()
|
|
|
|
cephalosporins_3rd()
|
|
|
|
cephalosporins_4th()
|
|
|
|
cephalosporins_5th()
|
|
|
|
fluoroquinolones()
|
|
|
|
glycopeptides()
|
|
|
|
macrolides()
|
|
|
|
penicillins()
|
|
|
|
tetracyclines()
|
|
}
|
|
\arguments{
|
|
\item{ab_class}{an antimicrobial class, like \code{"carbapenems"}. The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched (case-insensitive) for this value.}
|
|
}
|
|
\description{
|
|
Use these selection helpers inside any function that allows \href{https://tidyselect.r-lib.org/reference/language.html}{Tidyverse selections}, like \code{dplyr::select()} or \code{tidyr::pivot_longer()}. They help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.
|
|
}
|
|
\details{
|
|
All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.). This means that a selector like e.g. \code{\link[=aminoglycosides]{aminoglycosides()}} will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
|
|
|
|
These functions only work if the \code{tidyselect} package is installed, that comes with the \code{dplyr} package. An error will be thrown if \code{tidyselect} package is not installed, or if the functions are used outside a function that allows Tidyverse selections like \code{select()} or \code{pivot_longer()}.
|
|
}
|
|
\examples{
|
|
if (require("dplyr")) {
|
|
|
|
# this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
|
|
example_isolates \%>\%
|
|
select(carbapenems())
|
|
|
|
# this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
|
|
example_isolates \%>\%
|
|
select(mo, aminoglycosides())
|
|
|
|
# this will select columns 'mo' and all antimycobacterial drugs ('RIF'):
|
|
example_isolates \%>\%
|
|
select(mo, ab_class("mycobact"))
|
|
|
|
|
|
# get bug/drug combinations for only macrolides in Gram-positives:
|
|
example_isolates \%>\%
|
|
filter(mo_gramstain(mo) \%like\% "pos") \%>\%
|
|
select(mo, macrolides()) \%>\%
|
|
bug_drug_combinations() \%>\%
|
|
format()
|
|
|
|
|
|
data.frame(irrelevant = "value",
|
|
J01CA01 = "S") \%>\% # ATC code of ampicillin
|
|
select(penicillins()) # so the 'J01CA01' column is selected
|
|
|
|
}
|
|
}
|
|
\seealso{
|
|
\code{\link[=filter_ab_class]{filter_ab_class()}} for the \code{filter()} equivalent.
|
|
}
|